CUTD_OLEA2
ID CUTD_OLEA2 Reviewed; 310 AA.
AC Q30W71;
DT 16-MAR-2016, integrated into UniProtKB/Swiss-Prot.
DT 19-OCT-2011, sequence version 2.
DT 03-AUG-2022, entry version 107.
DE RecName: Full=Choline trimethylamine-lyase activating enzyme {ECO:0000255|HAMAP-Rule:MF_02059, ECO:0000303|PubMed:23151509};
DE EC=1.97.1.- {ECO:0000255|HAMAP-Rule:MF_02059, ECO:0000305|PubMed:23151509};
DE AltName: Full=Choline utilization protein D {ECO:0000255|HAMAP-Rule:MF_02059, ECO:0000303|PubMed:23151509};
DE AltName: Full=GRE activase CutD {ECO:0000255|HAMAP-Rule:MF_02059, ECO:0000303|PubMed:24854437};
DE AltName: Full=Glycyl-radical enzyme activating enzyme CutD {ECO:0000255|HAMAP-Rule:MF_02059, ECO:0000303|PubMed:23151509};
DE Short=GRE activating enzyme CutD {ECO:0000255|HAMAP-Rule:MF_02059, ECO:0000303|PubMed:24854437};
GN Name=cutD {ECO:0000255|HAMAP-Rule:MF_02059, ECO:0000303|PubMed:23151509};
GN OrderedLocusNames=Dde_3281 {ECO:0000312|EMBL:ABB40075.2};
OS Oleidesulfovibrio alaskensis (strain ATCC BAA-1058 / DSM 17464 / G20)
OS (Desulfovibrio alaskensis).
OC Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales;
OC Desulfovibrionaceae; Oleidesulfovibrio.
OX NCBI_TaxID=207559;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-1058 / DSM 17464 / G20;
RX PubMed=21685289; DOI=10.1128/jb.05400-11;
RA Hauser L.J., Land M.L., Brown S.D., Larimer F., Keller K.L.,
RA Rapp-Giles B.J., Price M.N., Lin M., Bruce D.C., Detter J.C., Tapia R.,
RA Han C.S., Goodwin L.A., Cheng J.F., Pitluck S., Copeland A., Lucas S.,
RA Nolan M., Lapidus A.L., Palumbo A.V., Wall J.D.;
RT "Complete genome sequence and updated annotation of Desulfovibrio
RT alaskensis G20.";
RL J. Bacteriol. 193:4268-4269(2011).
RN [2]
RP IDENTIFICATION, FUNCTION, AND PATHWAY.
RC STRAIN=ATCC BAA-1058 / DSM 17464 / G20;
RX PubMed=23151509; DOI=10.1073/pnas.1215689109;
RA Craciun S., Balskus E.P.;
RT "Microbial conversion of choline to trimethylamine requires a glycyl
RT radical enzyme.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:21307-21312(2012).
RN [3]
RP FUNCTION AS A RADICAL SAM ENZYME, CATALYTIC ACTIVITY, SUBUNIT, AND
RP COFACTOR.
RC STRAIN=ATCC BAA-1058 / DSM 17464 / G20;
RX PubMed=24854437; DOI=10.1021/cb500113p;
RA Craciun S., Marks J.A., Balskus E.P.;
RT "Characterization of choline trimethylamine-lyase expands the chemistry of
RT glycyl radical enzymes.";
RL ACS Chem. Biol. 9:1408-1413(2014).
CC -!- FUNCTION: Catalyzes activation of the choline trimethylamine-lyase CutC
CC under anaerobic conditions by generation of an organic free radical on
CC a glycine residue, via a homolytic cleavage of S-adenosyl-L-methionine
CC (SAM). Is involved in the anaerobic choline utilization pathway that
CC allows D.alaskensis to grow on choline as a source of carbon and
CC energy. {ECO:0000269|PubMed:23151509, ECO:0000269|PubMed:24854437}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=glycyl-[protein] + reduced [flavodoxin] + S-adenosyl-L-
CC methionine = 5'-deoxyadenosine + glycin-2-yl radical-[protein] + H(+)
CC + L-methionine + semiquinone [flavodoxin]; Xref=Rhea:RHEA:61976,
CC Rhea:RHEA-COMP:10622, Rhea:RHEA-COMP:14480, Rhea:RHEA-COMP:15993,
CC Rhea:RHEA-COMP:15994, ChEBI:CHEBI:15378, ChEBI:CHEBI:17319,
CC ChEBI:CHEBI:29947, ChEBI:CHEBI:32722, ChEBI:CHEBI:57618,
CC ChEBI:CHEBI:57844, ChEBI:CHEBI:59789, ChEBI:CHEBI:140311;
CC Evidence={ECO:0000305|PubMed:23151509};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02059,
CC ECO:0000269|PubMed:24854437};
CC Note=Binds 2 [4Fe-4S] clusters (PubMed:24854437). One cluster is
CC coordinated with 3 cysteines and an exchangeable S-adenosyl-L-
CC methionine (Probable). {ECO:0000269|PubMed:24854437, ECO:0000305};
CC -!- PATHWAY: Amine and polyamine metabolism; choline degradation.
CC {ECO:0000255|HAMAP-Rule:MF_02059, ECO:0000269|PubMed:23151509}.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:24854437}.
CC -!- SIMILARITY: Belongs to the organic radical-activating enzymes family.
CC {ECO:0000255|HAMAP-Rule:MF_02059, ECO:0000305}.
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DR EMBL; CP000112; ABB40075.2; -; Genomic_DNA.
DR AlphaFoldDB; Q30W71; -.
DR SMR; Q30W71; -.
DR STRING; 207559.Dde_3281; -.
DR EnsemblBacteria; ABB40075; ABB40075; Dde_3281.
DR KEGG; dde:Dde_3281; -.
DR eggNOG; COG1180; Bacteria.
DR HOGENOM; CLU_058969_0_0_7; -.
DR BioCyc; MetaCyc:MON-17847; -.
DR UniPathway; UPA01069; -.
DR Proteomes; UP000002710; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:UniProtKB.
DR GO; GO:0043364; F:glycyl-radical enzyme activating activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:1904047; F:S-adenosyl-L-methionine binding; IDA:UniProtKB.
DR GO; GO:0042426; P:choline catabolic process; IDA:UniProtKB.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_02059; Activ_enz_CutD; 1.
DR InterPro; IPR017896; 4Fe4S_Fe-S-bd.
DR InterPro; IPR017900; 4Fe4S_Fe_S_CS.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR040074; BssD/PflA/YjjW.
DR InterPro; IPR030905; CutC_activ_rSAM.
DR InterPro; IPR034457; Organic_radical-activating.
DR InterPro; IPR012839; Organic_radical_activase.
DR InterPro; IPR001989; Radical_activat_CS.
DR InterPro; IPR007197; rSAM.
DR PANTHER; PTHR30352; PTHR30352; 1.
DR Pfam; PF13187; Fer4_9; 1.
DR Pfam; PF04055; Radical_SAM; 1.
DR PIRSF; PIRSF000371; PFL_act_enz; 1.
DR SFLD; SFLDG01118; activating_enzymes__group_2; 1.
DR SFLD; SFLDS00029; Radical_SAM; 1.
DR TIGRFAMs; TIGR04395; cutC_activ_rSAM; 1.
DR PROSITE; PS00198; 4FE4S_FER_1; 2.
DR PROSITE; PS51379; 4FE4S_FER_2; 2.
DR PROSITE; PS01087; RADICAL_ACTIVATING; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Iron; Iron-sulfur; Metal-binding; Oxidoreductase;
KW Reference proteome; Repeat; S-adenosyl-L-methionine.
FT CHAIN 1..310
FT /note="Choline trimethylamine-lyase activating enzyme"
FT /id="PRO_0000435666"
FT DOMAIN 17..304
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT DOMAIN 48..77
FT /note="4Fe-4S ferredoxin-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT DOMAIN 79..109
FT /note="4Fe-4S ferredoxin-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT BINDING 31
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250|UniProtKB:P0A9N4, ECO:0000255|HAMAP-
FT Rule:MF_02059"
FT BINDING 35
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250|UniProtKB:P0A9N4, ECO:0000255|HAMAP-
FT Rule:MF_02059"
FT BINDING 37..39
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P0A9N4, ECO:0000255|HAMAP-
FT Rule:MF_02059"
FT BINDING 38
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250|UniProtKB:P0A9N4, ECO:0000255|HAMAP-
FT Rule:MF_02059"
FT BINDING 57
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02059, ECO:0000305"
FT BINDING 60
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02059, ECO:0000305"
FT BINDING 63
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02059, ECO:0000305"
FT BINDING 99
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02059, ECO:0000305"
FT BINDING 139
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P0A9N4, ECO:0000255|HAMAP-
FT Rule:MF_02059"
FT BINDING 188..190
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P0A9N4, ECO:0000255|HAMAP-
FT Rule:MF_02059"
FT BINDING 264
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P0A9N4, ECO:0000255|HAMAP-
FT Rule:MF_02059"
SQ SEQUENCE 310 AA; 34821 MW; BA334312AA784A52 CRC64;
MIERKALIFN IQKYNMYDGP GVRTLVFFKG CPLRCKWCSN PEGQLRQYQV LYKENLCVHC
GACVPVCPAG VHTISASTLR HGFAEGAQCI GCRRCEDVCP SSALAVVGEQ KTISELLEVI
EEDRPFYETS GGGVTLGGGE VLMQPEAAVN LLAACKQHGI NTAIETCGYA KQEVVMKAAQ
YVDLFLYDVK HIDSARHYEL TGVRNELILS NLTWLLENKH NVKIRVPLLR GVNDSEDDLR
GLVEYLRPYQ DYKNFKGIDL LPYHKMGVGK YKQLGWEYPI EGNPALSDAD LERVEACIRK
YDFPVSVIRH
